Sample summary
Basic statistics
Number of runs: 1
Number of samples (input count >0): 341
Number of controls: 0 3 samples with <1M reads after quality
filtering in taxonomy module excluded (M001BS3, M077BS3, and
M104BS3)
Sample type by country (includes replicates)
India Malawi
BS3 283 58Minimum, median, and maximum output counts by country
country n min med max
1 India 283.0 999999.1 1000000.0 1000000.9
2 Malawi 58.0 999999.2 1000000.0 1000000.6Summary of input biom - ps1
- n samples: 341
- n features: 2387
- total reads (million): 341
- mean % reads unmapped: 14.1
- mean % reads unintegrated: 72.9
- mean % reads mapped: 13
No additional filtering required given that normalised pathway data (copies per million) serves as input.
Unsupervised clustering
Clustering of samples (columns) and pathways (rows) - presence/absence
Clustering of samples (columns) and pathways (rows) - scaled asin-sqrt transformed relative abundances
Heatmap with cluster assignments
Correlation structure of scaled asin-sqrt transformed relative abundances (Spearman’s rank)
Number of functional pathways included: 2387
Number of samples included: 341
Session info
R version 4.2.1 (2022-06-23)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur ... 10.16
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] Maaslin2_1.10.0 FSA_0.9.3 ALDEx2_1.28.1
[4] zCompositions_1.4.0-1 truncnorm_1.0-8 NADA_1.6-1.1
[7] survival_3.4-0 MASS_7.3-58.1 sjstats_0.18.1
[10] ggExtra_0.10.0 formattable_0.2.1 inlmisc_0.5.5
[13] wesanderson_0.3.6 phangorn_2.10.0 ape_5.6-2
[16] DECIPHER_2.24.0 RSQLite_2.2.18 Biostrings_2.64.1
[19] GenomeInfoDb_1.32.4 XVector_0.36.0 IRanges_2.30.1
[22] S4Vectors_0.34.0 BiocGenerics_0.42.0 cowplot_1.1.1
[25] scales_1.2.1 RVAideMemoire_0.9-81-2 DescTools_0.99.47
[28] ggsignif_0.6.4 binom_1.1-1.1 shiny_1.7.3
[31] randomcoloR_1.1.0.1 crossval_1.0.4 labdsv_2.0-1
[34] mgcv_1.8-41 nlme_3.1-160 ggpubr_0.4.0
[37] data.table_1.14.4 corrplot_0.92 vegan_2.6-4
[40] lattice_0.20-45 permute_0.9-7 randomForest_4.7-1.1
[43] matrixStats_0.62.0 lme4_1.1-30 Matrix_1.5-1
[46] reshape2_1.4.4 pheatmap_1.0.12 DT_0.26
[49] plotly_4.10.0 cluster_2.1.4 tidyr_1.2.1
[52] dplyr_1.0.10 magrittr_2.0.3 plyr_1.8.7
[55] kableExtra_1.3.4 gridExtra_2.3 RColorBrewer_1.1-3
[58] knitr_1.40 ggplot2_3.3.6 phyloseq_1.40.0
loaded via a namespace (and not attached):
[1] estimability_1.4.1 coda_0.19-4
[3] bit64_4.0.5 DelayedArray_0.22.0
[5] RCurl_1.98-1.9 generics_0.1.3
[7] terra_1.6-17 proxy_0.4-27
[9] bit_4.0.4 webshot_0.5.4
[11] xml2_1.3.3 httpuv_1.6.6
[13] SummarizedExperiment_1.26.1 assertthat_0.2.1
[15] xfun_0.34 jquerylib_0.1.4
[17] evaluate_0.17 promises_1.2.0.1
[19] DEoptimR_1.0-11 fansi_1.0.3
[21] readxl_1.4.1 igraph_1.3.5
[23] DBI_1.1.3 htmlwidgets_1.5.4
[25] purrr_0.3.5 ellipsis_0.3.2
[27] backports_1.4.1 V8_4.2.1
[29] insight_0.18.6 MatrixGenerics_1.8.1
[31] vctrs_0.5.0 Biobase_2.56.0
[33] sjlabelled_1.2.0 abind_1.4-5
[35] cachem_1.0.6 withr_2.5.0
[37] robustbase_0.95-0 rgdal_1.5-32
[39] emmeans_1.8.2 getopt_1.20.3
[41] svglite_2.1.0 lazyeval_0.2.2
[43] crayon_1.5.2 flexdashboard_0.6.0
[45] pkgconfig_2.0.3 rlang_1.0.6
[47] lifecycle_1.0.3 miniUI_0.1.1.1
[49] modelr_0.1.9 cellranger_1.1.0
[51] datawizard_0.6.3 raster_3.6-3
[53] carData_3.0-5 lpsymphony_1.24.0
[55] Rhdf5lib_1.18.2 boot_1.3-28
[57] viridisLite_0.4.1 parameters_0.19.0
[59] rootSolve_1.8.2.3 bitops_1.0-7
[61] rhdf5filters_1.8.0 blob_1.2.3
[63] stringr_1.4.1 rstatix_0.7.0
[65] memoise_2.0.1 zlibbioc_1.42.0
[67] compiler_4.2.1 cli_3.4.1
[69] ade4_1.7-19 tidyselect_1.2.0
[71] stringi_1.7.8 highr_0.9
[73] yaml_2.3.6 grid_4.2.1
[75] sass_0.4.2 fastmatch_1.1-3
[77] tools_4.2.1 lmom_2.9
[79] rstudioapi_0.14 foreach_1.5.2
[81] optparse_1.7.3 gld_2.6.6
[83] farver_2.1.1 Rtsne_0.16
[85] RcppZiggurat_0.1.6 digest_0.6.30
[87] quadprog_1.5-8 Rcpp_1.0.9
[89] GenomicRanges_1.48.0 car_3.1-1
[91] broom_1.0.1 performance_0.10.0
[93] later_1.3.0 httr_1.4.4
[95] effectsize_0.8.1 colorspace_2.0-3
[97] rvest_1.0.3 splines_4.2.1
[99] expm_0.999-6 sp_1.5-0
[101] multtest_2.52.0 Exact_3.2
[103] systemfonts_1.0.4 xtable_1.8-4
[105] jsonlite_1.8.3 nloptr_2.0.3
[107] Rfast_2.0.6 R6_2.5.1
[109] pillar_1.8.1 htmltools_0.5.3
[111] mime_0.12 glue_1.6.2
[113] fastmap_1.1.0 minqa_1.2.5
[115] BiocParallel_1.30.4 class_7.3-20
[117] codetools_0.2-18 pcaPP_2.0-3
[119] mvtnorm_1.1-3 utf8_1.2.2
[121] bslib_0.4.0 tibble_3.1.8
[123] curl_4.3.3 biglm_0.9-2.1
[125] rmarkdown_2.17 biomformat_1.24.0
[127] munsell_0.5.0 e1071_1.7-12
[129] rhdf5_2.40.0 GenomeInfoDbData_1.2.8
[131] iterators_1.0.14 sjmisc_2.8.9
[133] gtable_0.3.1 bayestestR_0.13.0 .